Chemical Components in the PDB

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AN6 : Summary

Code

AN6

One-letter code

L

Molecule name

5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine

Systematic names

ProgramVersionName
ACDLabs 11.02 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine
OpenEye OEToolkits 1.6.1 (2S)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl-ethyl-amino]-2-azanyl-butanoic acid

Formula

C16 H25 N7 O5

Formal charge

0

Molecular weight

395.414 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 11.02 O=C(O)C(N)CCN(CC)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
SMILES CACTVS 3.352 CCN(CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 1.7.0 CCN(CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Canonical SMILES CACTVS 3.352 CCN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
Canonical SMILES OpenEye OEToolkits 1.7.0 CC[N@@](CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O

IUPAC InChI

InChI=1S/C16H25N7O5/c1-2-22(4-3-8(17)16(26)27)5-9-11(24)12(25)15(28-9)23-7-21-10-13(18)19-6-20-14(10)23/h6-9,11-12,15,24-25H,2-5,17H2,1H3,(H,26,27)(H2,18,19,20)/t8-,9+,11+,12+,15+/m0/s1

IUPAC InChI key

GAMUFACDOHMHSZ-OPYVMVOTSA-N
AN6

wwPDB Information

Atom count

53 (28 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

LEU

Defined at

2009-07-28

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



AN6 : Atoms of Molecule

Total Number of Atoms: 53
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C' C C' N N N 0 -4.898 -2.627 -0.872
2 N' N N' N N N 0 -5.82 -1.388 1.004
3 O' O O' N N N 0 -4.941 -3.605 -0.164
4 C1 C C1 N N N 0 -3.347 2.309 2.962
5 N1 N N1 N Y N 0 6.073 -1.351 0.479
6 C2 C C2 N Y N 0 5.859 -0.049 0.426
7 C3 C C3 N N N 0 -2.905 2.699 1.55
8 N3 N N3 N Y N 0 4.652 0.465 0.325
9 C4 C C4 N Y N 0 3.582 -0.322 0.271
10 C5 C C5 N Y N 0 3.757 -1.715 0.324
11 C6 C C6 N Y N 0 5.065 -2.216 0.432
12 N6 N N6 N N N 0 5.299 -3.579 0.489
13 N7 N N7 N Y N 0 2.525 -2.275 0.253
14 C8 C C8 N Y N 0 1.628 -1.336 0.162
15 N9 N N9 N Y N 0 2.23 -0.114 0.169
16 C1' C C1' R N N 0 1.557 1.185 0.084
17 N10 N N10 N N N 0 -2.716 1.485 0.744
18 C2' C C2' R N N 0 1.472 1.66 -1.389
19 O2' O O2' N N N 0 2.658 2.361 -1.768
20 C3' C C3' S N N 0 0.254 2.615 -1.352
21 O3' O O3' N N N 0 0.686 3.972 -1.236
22 C4' C C4' R N N 0 -0.523 2.187 -0.092
23 O4' O O4' N N N 0 0.175 1.068 0.484
24 C5' C C5' N N N 0 -1.947 1.777 -0.473
25 O5' O O5' N N N 0 -4.655 -2.76 -2.186
26 CA' C CA' S N N 0 -5.123 -1.259 -0.283
27 CB' C CB' N N N 0 -3.774 -0.57 -0.064
28 CG' C CG' N N N 0 -4.006 0.864 0.417
29 HN' H HN' N N N 0 -6.741 -1.782 0.878
30 HN'A H HN'A N N N 0 -5.278 -1.936 1.655
31 H1 H H1 N N N 0 -4.33 1.84 2.919
32 H1A H H1A N N N 0 -2.629 1.609 3.388
33 H1B H H1B N N N 0 -3.398 3.201 3.586
34 H2 H H2 N N N 0 6.707 0.619 0.467
35 H3 H H3 N N N 0 -3.67 3.325 1.09
36 H3A H H3A N N N 0 -1.967 3.25 1.603
37 HN6 H HN6 N N N 0 4.555 -4.201 0.454
38 HN6A H HN6A N N N 0 6.207 -3.913 0.563
39 H8 H H8 N N N 0 0.563 -1.502 0.091
40 H1' H H1' N N N 0 2.073 1.924 0.697
41 H2' H H2' N N N 0 1.288 0.82 -2.058
42 HO2' H HO2' N N N 0 2.652 2.678 -2.681
43 H3' H H3' N N N 0 -0.36 2.485 -2.243
44 HO3' H HO3' N N N 0 1.229 4.276 -1.975
45 H4' H H4' N N N 0 -0.553 3.009 0.623
46 H5' H H5' N N N 0 -1.913 0.888 -1.103
47 H5'A H H5'A N N N 0 -2.426 2.59 -1.019
48 HO5' H HO5' N N N 0 -4.517 -3.658 -2.518
49 HA' H HA' N N N 0 -5.728 -0.664 -0.966
50 HB' H HB' N N N 0 -3.204 -1.117 0.686
51 HB'A H HB'A N N N 0 -3.219 -0.553 -1.002
52 HG' H HG' N N N 0 -4.639 0.852 1.304
53 HG'A H HG'A N N N 0 -4.495 1.437 -0.371



AN6 : Chemical Bonds

Total Number of Bonds: 55
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O' C' O C doub 1.21 N N
2 C' O5' C O sing 1.34 N N
3 C' CA' C C sing 1.51 N N
4 N' CA' N C sing 1.47 N N
5 N' HN' N H sing 1.01 N N
6 N' HN'A N H sing 1.01 N N
7 C1 C3 C C sing 1.53 N N
8 C1 H1 C H sing 1.09 N N
9 C1 H1A C H sing 1.09 N N
10 C1 H1B C H sing 1.09 N N
11 C6 N1 C N doub 1.33 N Y
12 N1 C2 N C sing 1.32 N Y
13 N3 C2 N C doub 1.32 N Y
14 C2 H2 C H sing 1.08 N N
15 C3 N10 C N sing 1.47 N N
16 C3 H3 C H sing 1.09 N N
17 C3 H3A C H sing 1.09 N N
18 C4 N3 C N sing 1.33 N Y
19 N9 C4 N C sing 1.37 N Y
20 C5 C4 C C doub 1.4 N Y
21 N7 C5 N C sing 1.36 N Y
22 C5 C6 C C sing 1.4 N Y
23 N6 C6 N C sing 1.38 N N
24 N6 HN6 N H sing 0.97 N N
25 N6 HN6A N H sing 0.97 N N
26 C8 N7 C N doub 1.3 N Y
27 C8 N9 C N sing 1.36 N Y
28 C8 H8 C H sing 1.08 N N
29 N9 C1' N C sing 1.47 N N
30 O4' C1' O C sing 1.44 N N
31 C2' C1' C C sing 1.55 N N
32 C1' H1' C H sing 1.09 N N
33 CG' N10 C N sing 1.47 N N
34 N10 C5' N C sing 1.47 N N
35 C3' C2' C C sing 1.55 N N
36 C2' O2' C O sing 1.43 N N
37 C2' H2' C H sing 1.09 N N
38 O2' HO2' O H sing 0.97 N N
39 C4' C3' C C sing 1.54 N N
40 C3' O3' C O sing 1.43 N N
41 C3' H3' C H sing 1.09 N N
42 O3' HO3' O H sing 0.97 N N
43 C5' C4' C C sing 1.53 N N
44 O4' C4' O C sing 1.44 N N
45 C4' H4' C H sing 1.09 N N
46 C5' H5' C H sing 1.09 N N
47 C5' H5'A C H sing 1.09 N N
48 O5' HO5' O H sing 0.97 N N
49 CB' CA' C C sing 1.53 N N
50 CA' HA' C H sing 1.09 N N
51 CG' CB' C C sing 1.53 N N
52 CB' HB' C H sing 1.09 N N
53 CB' HB'A C H sing 1.09 N N
54 CG' HG' C H sing 1.09 N N
55 CG' HG'A C H sing 1.09 N N



AN6 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
AN6 3p71 Open in New Window Bound ligand 1 1
AN6 6wj7 Open in New Window Bound ligand 1 1